Parrington addresses this issue on page 63 by describing experiments from the late 1960s showing that there was a great deal of noncoding DNA in our genome and that only a few percent of the genome was devoted to encoding proteins. He also notes that the differences in genome sizes of similar species gave rise to the possibility that most of our genome was junk. Five pages later (page 69) he reports that scientists were surprised to find only 30,000 protein-coding genes when the sequence of the human genome was published—"... the other big surprise was how little of our genomes are devoted to protein-coding sequence."

Contradictory stuff like that makes it every hard to follow his argument. On the one hand, he recognizes that scientists have known for 50 years that only 2% of our genome encodes proteins but, on the other hand, they were "surprised" to find this confirmed when the human genome sequence was published.

He spends a great deal of Chapter 4 explaining the existence of introns and claims that "over 90 per cent of our genes are alternatively spliced" (page 66). This seems to be offered as an explanation for all the excess noncoding DNA but he isn't explicit.

In spite of the fact that genome comparisons are a very important part of this debate, Parrington doesn't return to this point until Chapter 10 ("Code, Non-code, Garbage, and Junk").

We know that the C-Value Paradox isn't really a paradox because most of the excess DNA in various genomes is junk. There isn't any other explanation that makes sense of the data. I don't think Parrington appreciates the significance of this explanation.

The examples quoted in Chapter 10 are the lungfish, with a huge genome, and the pufferfish (Fugu), with a genome much smaller than ours. This requires an explanation if you are going to argue that most of the human genome is functional. Here's Parrington's explanation ...

Yet, despite having a genome only one eighth the size of ours, Fugu possesses a similar number of genes. This disparity raises questions about the wisdom of assigning functionality to the vast majority of the human genome, since, by the same token, this could imply that lungfish are far more complex than us from a genomic perspective, while the smaller amount of non-protein-coding DNA in the Fugu genome suggests the loss of such DNA is perfectly compatible with life in a multicellular organism.

Not everyone is convinced about the value of these examples though, John Mattick, for instance, believes that organisms with a much greater amount of DNA than humans can be dismissed as exceptions because they are 'polyploid', that is, their cells have far more than the normal two copies of each gene, or their genomes contain an unusually high proportion of inactive transposons.

In other words, organisms with larger genomes seem to be perfectly happy carrying around a lot of junk DNA! What kind of an argument is that?

Mattick is also not convinced that Fugu provides a good example of a complex organism with no non-coding DNA. Instead, he points out that 89% of this pufferfish's DNA is still non-protein-coding, so the often-made claim that this is an example of a multicellular organism without such DNA is misleading.

[Mattick has been] a true visionary in his field; he has demonstrated an extraordinary degree of perseverance and ingenuity in gradually proving his hypothesis over the course of 18 years.
Hugo Award Committee Seriously? That's the best argument he has? He and Mattick misrepresent what scientists say about the pufferfish genome—nobody claims that the entire genome encodes proteins—then they ignore the main point; namely, why do humans need so much more DNA? Is it because we are polyploid?

You know, as irriitating as the IDiots and other creationists can be, these examples of misunderstandings by scientists and science writers who supposedly are not encumbered by superstitious beliefs are even more depressing. In the examples above, the errors of Mattick and Parrington are not due to ignorance, but stem from a simple inability to follow the logic of an argument. The lack of basic critical thinking skills, IOW. How is this possible in people so highly educated?

I agree. I'm positively flabbergasted by this. I suspect they are simply not aware of the force of these arguments, they are only superficially familiar with them and just haven't bothered thinking about it, instead just following along with the hype mindlessly thinking they are at the forefront of science.

I mean that has to be it, because the alternative is that they are either stupid or engaging in deliberate misinformation.

I dunno why that posted twice and with errors. I'll try again: Larry you really should write a book about this. There are too many shitty books on junk DNA now by hyping know-nothings. Get together with some people who know their stuff (Graur, Lynch? I'm sure you know some people), that know how to accurately present all of the information, both for and against, and write one.

If you're not going to write it, who is? The molecular biology community seems to be in dire need of such a book. :)

But, but, but -- The South African Lungfish with 3540% the DNA content of "mammals" is a diploid with 2n = 34. Not polyploid. Did he mean that it's a diploidized ancient polyploid? Or is this a mistake? Or is this the result of knowing that at least one lungfish is tetraploid (2n - 68) and one has 2n = 54, plus assuming this means that all the high-DNA-content lungfishes are polyploid? By the way, lunglfish, or at least one lungfish species, have a LOT of old, mutated transposons.

Okay, perhaps I don't understand the point that Parrington is trying to make, but how is acknowledging that large genomes often "contain an unusually high proportion of inactive transposons" a solid argument against the notion that much of the genome is non-functional? It seems to imply the opposite to me...

Many of the arguments appear a bit confused to me, but because I am not myself a genome researcher I cannot judge beyond "given everything else I know about biology, this sounds more plausible to me than the opposite". However, even apart from the issues already pointed out in the post the following really stands out to me because I have done cytology on polyploid plants and read a lot about the matter:

John Mattick, for instance, believes that organisms with a much greater amount of DNA than humans can be dismissed as exceptions because they are 'polyploid', that is, their cells have far more than the normal two copies of each gene

How is that supposed to work? When a polyploidy event happens, everything gets duplicated. That means that at that moment, the ratios between different genomic elements are precisely the same.

In most polyploid plants, the next step seems to be quite some selective pressure to downsize the genome: tetraploids are often less than 2x as big as diploids, and octoploids are again often less than 2x as big as tetraploids, and so on. (There are exceptions.) It seems logical to assume that a lot of what will be thrown out was junk in the first place but also, at least in the long run, and unless the plant really needs another 20k functional genes with a specialised function - an a priori extremely implausible suggestion - everything but two functional copies of each gene.

Also, the logic of the argument seems to assume that the small, mean and lean genomes are the polyploids ones... but of course within each group of closely related species the big ones are polyploid.

Some massive genomes are polyploid, but that does not explain all of their DNA content.

Here is an example of the limited success we've had so far sequencing huge genomes

http://www.genomebiology.com/2014/15/3/R59

23.2Gb, 82% repeats.

Note, of course, that ancient polyploidization and massive expansion of repetitive elements are not mutually exclusive, they can and do *both occur

The most interesting organisms with respect to that question are dinoflagellates - single-celled, but with massive genomes (up to 200Gb), and they're not polypoloid (they also have many many extremely weird features, but let's just talk about genome size and content). Why? The working model based on sequencing small pieces of DNA has been that genes in dinoflagellates exist in tandem arrays of multiple copies of the same gene. But that's not really what they found when they partially sequenced one of the smallest genomes in the group. So lots of unknowns there. Anyway. theory predicts that such genomes would arise if the effective population size is low. However, that is usually not the case for single-celled algae with huge absolute populations. And there have been very few studies of N_e in dinoflagellates (I am aware of one study that tried to estimate it, and the estimate was indeed very low). So if when the 100Gb dinoflagellate genomes are sequenced one day, and if they turn out to be full of apparent "junk", and it turns out that N_e is indeed very low for some weird reason, the proponents of the view that there is no junk DNA will have a lot of explaining to do - if all that complexity is what it takes to make a human, why do protists exhibit it too? That argument would apply even if it turned out that the more massive representatives of those genomes are indeed mostly tandem arrays of the same genes without a lot of TEs and intergenic DNA, because there is a lot of evidence, from multiple protists in fact, that epigenetic mechanisms, which are a big topic of the book we're discussing, are even more complex in some unicellular organisms than they are in humans.

Just because a DNA doesn't seem translationally or transcriptionally active does not mean it can't be active in terms of regulation, providing redundancy, providing a means of adaptive variation, having structural roles, roles in cellular differentiation, or in one case optical roles.

Sternberg points out:

"Why the elaborate repositioning of so much "junk" DNA in the rod cells of nocturnal mammals? The answer is optics. A central cluster of chromocenters surrounded by a layer of LINE-dense heterochromatin enables the nucleus to be a converging lens for photons, so that the latter can pass without hindrance to the rod outer segments that sense light. In other words, the genome regions with the highest refractive index -- undoubtedly enhanced by the proteins bound to the repetitive DNA -- are concentrated in the interior, followed by the sequences with the next highest level of refractivity, to prevent against the scattering of light. The nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light.

So the next time someone tells you that it "strains credulity" to think that more than a few pieces of "junk DNA" could be functional in the cell -- that the data only point to the lack of design and suboptimality -- remind them of the rod cell nuclei of the humble mouse."

Given that DNA may have more than just a coding role but may even have gotten recruited for such unexpected roles like being a lens, the C-value paradox might be explainable by the fact that DNA might have unique applications in a variety of organisms than just mere coding for proteins. Large or small amounts of DNA that have function may or may not contribute to the overall complexity of the organism because the excess may not necessarily be for coding functions.

Junk in one organism doesn't imply junk in another. So ENCODE could be right about the human genome even if Ferns have junk DNA....

There is the phenomenon of redundancy whereby duplicates provide function in the way or redundancy, and so extra DNA not immediately used is not necessarily an indication it is junk.

The central dogma does not necessarily imply all the information for life resides in the DNA, especially ontogenic information. Some candidates for other information storage mechanisms apart from DNA are the glyco protein complexes that implement the "sugar code". Hence the information that creates the complexity of an organism might be outside the nuclear complex, and thus there is no necessity that DNA be larger for more complex organisms if most of the information to generate that complexity lies outside the nuclear complex.

Since the information processing of DNA is not restricted to ACGTs only, but also methylation marks and indirectly histone modifications, large amounts of nuclear DNA might be the normal way an organism's sugar code and other cytoplasmic memories recruit DNA.

And as pointed out with the mouse eye, junk DNA might have function in unexpected ways in various organisms.

It is really too early to insist that the C-value paradox is solved merely by invoking junk arguments.

"So the next time someone tells you that it "strains credulity" to think that more than a few pieces of "junk DNA" could be functional in the cell -- that the data only point to the lack of design and suboptimality -- remind them of the rod cell nuclei of the humble mouse."

So what you are trying to say is that if you knockout the so-called junk DNA in nocturnal mammals, they are going to be blind at night, which will decrease their fitness, which will be less likely for them to survive. Right?

I wonder what would happen and you would knockout so-called junk DNA from a human or a chimpanzee genome?

You're struggling with semantics, KevNick. If one says that no more than a few pieces of non-coding DNA serve a function, and therefore most of it is junk, it does not contradict this to demonstrate that a few pieces of non-coding DNA do serve a function.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.